Download Epistasis: Methods and Protocols by Jason H. Moore, Scott M. Williams PDF

By Jason H. Moore, Scott M. Williams

This quantity offers a helpful and quite simply reproducible number of demonstrated and rising concepts on sleek genetic analyses. Chapters specialise in statistical or facts mining analyses, genetic structure, the weight of a number of trying out, genetic variance, measuring epistasis, multifactor dimensionality aid, and ReliefF. Written within the hugely winning Methods in Molecular Biology sequence structure, chapters contain introductions to their respective issues, lists of the required fabrics and reagents, step by step, without difficulty reproducible laboratory protocols, and key pointers on troubleshooting and averting recognized pitfalls.

Authoritative and useful, Epistasis: equipment and Protocols aids scientists in carrying on with to review elucidate epistasis within the context of recent facts availability.

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Extra resources for Epistasis: Methods and Protocols

Sample text

While there have been over 150 loci identified for association with lipid traits, the proportion of heritability explained is still modest with ∼25–30 % of the genetic variance for each lipid trait [44, 45]. Due to this missing heritability, several groups have embarked on explorations of epistasis or gene–gene interactions in lipid traits. For example, Turner et al. looked for epistasis associated with HDL cholesterol [41] using a biological knowledge-driven filtering method. Here, the Biofilter [37, 38] was used to decrease the number of SNP–SNP models evaluated from genome-wide genotype data.

Maher B (2008) Personal genomes: the case of the missing heritability. Nature 456:18–21. 1038/456018a 2. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM (2009) Finding the missing heritability of complex diseases. Nature 461:747–753. 1038/ nature08494 3.

A number of alternative approaches are described, but the primary focus is on the use of prior biological knowledge from databases in the public domain to guide the search for epistasis. The manner in which prior knowledge is incorporated into a GWAS study can be done in several different ways and the knowledge can be extracted from a variety of database sources. These approaches will be discussed, and some successful applications will be described. Incorporating biological knowledge is likely to be fruitful in the search for epistasis in large-scale genomic studies of the current state-of-the-art and into the future.

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